ADVANCED BIOCHEMISTRY LABORATORY
BMB 471 SYLLABUS - SPRING 2016
A. Instructors
Faculty & Staff
Neil R. Bowlby
Kathleen Foley
R. Michael Garavito**
Heedeok Hong
Office
113 Biochemistry
302B Biochemistry
513 Biochemistry
325 Chemistry
Phone
353-8546
353-5561
355-9724
355-9715 ext 352
Office Hours*
10 - 12 noon Mon.
3:15 - 5:15 p.m. Mon.
10 - 11 a.m. Mon. & Fri.
Teaching Assistants
Office
Phone
Email
gaffne11@msu.edu
Kristen Gaffney
315 Chemistry
355-9715 ext 134
lavellan@msu.edu
Anastasiya Lavell
110 Plant Biology
763-957-0309
lotzsamu
@msu.edu
Sam Lotz
S220 Plant Biology
432-0071
rohnkebr @msu.edu
Brandon Rohnke
322 Plant Biology
353-3992
*students are welcome to come at other times, but should make an appointment.
**course coordinator
B. Books Used in Biochemistry and Molecular Biology 471
1. Texts
a. Required to be purchased by student:
(1) Advanced Biochemistry Laboratory, 2016 ed.
(2) Advanced Biochemistry Laboratory Supplement, 2016 ed. (Part of Advanced
Biochemistry Laboratory BMB 471 coursepack)
(3) Segel, I.H., Biochemical Calculations, 2nd ed., J. Wiley & Sons, Inc., 1976.
(4) Day, R.A., How to Write and Publish a Scientific Paper, 6th ed. Oryx Press,
2006.
b. Recommended to purchase:
(1) Boyer, R.F., Modern Experimental Biochemistry, 3rd ed., Addison Wesley Pub.
Co., 2000.
(2) Voet, D. and Voet, J.G., Biochemistry, 2nd edition, J. Wiley & Sons, N.Y., N.Y.,
1995.
2. Handbooks:
a. Handbook of Chemistry & Physics, CRC Press (various editions, a new edition is
published each year)
b. The Merck Index, Merck & Co. (various editions)
c. Dawson, R.M., Elliott, D.C., Elliott, W.H., and Jones, K.M., Data for Biochemical
Research, 3rd ed., Clarendon Press, Oxford, 1986.
d. Sax, N.I., Dangerous Properties of Industrial Materials, 4th or 5th ed., Van Nostrand
Reinhold Co., 1975 (4th), 1979 (5th)
e. Rayburn, S.R., The Foundations of Laboratory Safety, Springer-Verlag, 1990.
C. Objectives
The subject areas for the course are weak acids and bases, spectrophotometry, organelles and
lipids, and enzymes and other proteins. The objectives for the course are for students to:
1. Develop the ability to design logical experiments given specific experimental objectives
but only general procedures, perform these experiments successfully and independently,
properly interpret the data, and clearly present the data in writing.
2. Learn modern biochemical laboratory methodology and techniques.
3. Further develop:
a. quantitative laboratory skills.
b. the ability to keep a clear and complete lab notebook.
c. the ability to treat laboratory data.
d. skill in writing scientific laboratory reports.
4. Understand the concepts on which the laboratory experiments are based and related
concepts (largely covered in lecture and homework problems).
D. Organization of Course
The course consists of one 50-minute lecture/discussion period and one 5-hour laboratory
period per week. A pre-lab session will be held in Rm. 111 Biochemistry starting at 12:40 p.m.
of each scheduled lab period. The course will have a semi-open lab format; students may leave
and return to the lab rooms at any time. The labs (113 & 117 Biochemistry) will be open
Tuesday through Friday from 12:30 to 5:30 p.m., and students may work only on their scheduled
lab day.
Students work in teams of two on Units A, D, and E and individually in Units B, C, and F.
Students work in pairs only on the experimental (data acquisition) portion of Units A, D, and E;
notebook preparation, data analysis/post-lab notebook entries and lab reports are to be done
individually. Students are expected to perform experimental work each lab period. Except
in cases of excused absence, students who do not participate in data collection during the
lab period are not entitled to the data collected by others.
E. Ethics
Ethical behavior and academic integrity in this course are expected and assumed. The
consequences can be quite serious if these are not practiced. We will teach you accepted
standards of intellectual honesty with respect to the performance of experiments, the processing
of data, and the reporting of results. We expect you to follow these standards. Particularly be
aware of when you must work independently. Credit will not be given to work obtained through
collaboration when independent effort is required.
F. Computer Resources
The Biochemistry Computer Room is located in Room 105 (in the Undergraduate Office) of
the Biochemistry Building. This room contains four computers that have Windows and
Microsoft Office installed and are connected to several printers. These computers have
SIMZYME and Hyperbolic Regression as well as other programs useful to BMB 471 students.
All computers are available for your use when the office is open, normally between 8:00 a.m.
and 5:00 p.m., Monday-Friday. In addition, the Teaching Lab has computers in the lab that may
be used during scheduled laboratory hours.
We will be using the Desire2Learn (D2L) system for posting announcements and course
materials as well as for submission of text-only laboratory reports. Pre-lab problem sets will be
available on LON-CAPA according to the schedule posted in G.2.
G. Schedule and Dates for Experimental Work, Notebooks and Lab Reports, Pre-lab
problem sets, Discussion Sections and readings, and Final Exam
1. Experimental work, notebook and laboratory report due dates
Lab
Period
1
2
3
4
5
6
7
8
Experimental Work
Date
Due Dates
Lab introduction; check in; safety tour; student practice with
Jan. 12 - 15 spectrophotometers, including recorder set-up and operation
Jan. 19 - 22 Unit A - purity of light, wavelength accuracy, absorbance accuracy,
absorbance linearity, recorder use
Jan. 26 - 29 Unit B - buffer preparation; pH measurements
- effects of salt & dilution on pH of a buffer
Feb. 2 - 5
Unit C - FMN solution ppn. & standard curve data collection
Unit D - liver mitochondria preparation
- Lowry protein assay of liver mitochondria fractions
Unit D - thin layer chromatography / gas chromatography
Feb. 16 - 19
- SDH assay of liver fractions
Feb. 9 - 12
Feb. 8: Notebooks**
Units A-C
Feb. 15: Report I*
Units A-C
Feb. 23 - 26 Unit D - thin layer chromatography / gas chromatography
Mar. 1 - 4
Unit E - ammonium sulfate precipitation and AAT assays
Feb. 29: Notebooks**
Mar. 4: Report II*
Unit D
Mar. 7 - 11
Spring Break
9
Mar. 15 - 18 Unit E - CM-sephadex column chromatography
- Lowry protein assay of AAT fractions
10
Mar. 22 - 25 Unit E - SDS-PAGE of AAT fractions
Unit F - buffer/ethanol preparation, yADH assay testing
11
Mar. 29 Apr. 1
Unit F - [yADH], [NAD+], yADH stability
12
Apr. 5 - 8
Unit F - approximate Km & Vmax, stability
13
Apr. 12 - 15 Unit F - precise valid range, stability
14
Apr. 19 - 22 Unit F - precise Km & Vmax and inhibition, stability
15
Apr. 26 - 29 Lab check-out
Mar. 28:
Notebooks - Unit E**
April 4:
Report III - Unit E*
Apr. 25:Notebooks**
Apr. 29: Report IV*
Unit F
Final
Exam
Thursday May 5, 12:45 - 2:45 p.m. Location to be announced.
*submit reports by placing them in the wooden "Assignment Box" in Room 113, BCH Bldg.
REPORTS ARE DUE BY 2:00 p.m. - LATE REPORTS RECEIVE NO CREDIT
**lab notebooks must be submitted by 9:00 a.m. to be graded and returned by 12:40 of that day.
2. Pre-lab problem sets
A short problem set will be available through LON-CAPA on Mondays. The problems will
test your understanding of the experiments and the processing of the data collected for
experiments performed the following week. The assignments are due before the scheduled
start of the following week’s lecture (12:40 p.m.) on Mondays. The schedule for distribution
and due dates of the problems is as follows:
Post Date
January 11
January 18
January 25
February 1
February 8
February 15
February 22
February 29
March 14
March 21
March 28
April 4
April 11
Due Date
January 18
January 25
February 1
February 8
February 15
February 22
February 29
March 14
March 21
March 28
April 4
April 11
April 18
Material Covered
Unit A
Unit B
Unit C
Unit D - Day 1 (mito isol., Lowry assay)
Unit D - SDH assays, GC/TLC
Unit D - GC/TLC
Unit E - Day 1 (Pilot ppn., AAT assay)
Unit E - Day 2 (CM-sephadex, Lowry)
Unit E - Day 3 (SDS-PAGE, yADH buffers
Unit F - Day 1 (yADH assays)
Unit F - Day 2 (Approx. Km & Vmax)
Unit F - Day 3 (Valid Range)
Unit F - Day 4 (Prec. Km/Vmax, Inhib)
3. Discussion section schedule and readings.
(Mondays, 12:40 - 1:30 p.m., 101 Biochemistry)
Date
Subject
Reading
Jan. 11
Spectrophotometry,
including Beer's and
Lambert's laws
1. Experimental Biochemistry Supplement, Chapter 3.
2. Segel, I.H. Biochemical Calculations, 2nd ed., pp. 324 - 333
Jan. 25
Buffers, activity, and
related subjects
1. Experimental Biochemistry Supplement, Chapter 2.
2. Segel, I.H., Biochemical Calculations, 2nd ed. pp. 1-83.
Feb. 1
Standard curves
1. Experimental Biochemistry Supplement, Chapter 1.
Assay of enzymes
Isolation of Organelles
1. Experimental Biochemistry Supplement, Chapters 4 & 7.
Feb. 8, 15,
22
2. Segel, I.H., Bioch. Calcs., 2nd ed. pp. 208-214, 291-92, 341-46.
Chromatography/Lipids
Feb. 22
Protein purification
1. Experimental Biochemistry Supplement, Chapter 7.
2. Segel, I.H., Bioch. Calcs., 2nd ed. pp. 287-290, 333-341.
Feb. 29
Chromatography
1. Experimental Biochemistry Supplement, Chapter 6.
Mar. 14
SDS-PAGE/Protein
Assays
1. Experimental Biochemistry Supplement, Chapter 5.
Chemical and Enzyme
Kinetics
1. Experimental Biochemistry Supplement, Chapter 8.
Mar. 21, 28
April 4, 11
2. Segel, I.H., Biochemical Calculations, 2nd ed., pp. 208-212 (top), 214219, 221 (bottom)-236 plus problem 4.9 on page 237, 246-250, 252.
4. Final Exam: Thursday, May 5, 12:45 - 2:45 p.m. Location to be announced.
The exam will test your understanding of the quantitative and conceptual aspects of the
experimental work, the material covered in the discussion (lecture) periods and the assigned
readings, including pre-lab problems. Problems of the type encountered in the experimental
work and in the pre-lab problems may be on the exams. Other questions will involve a narrative
response.
Bring a calculator and transparent ruler to the final exam.
H. Grading
Grades will be based on the following items and approximate distribution of points:
Laboratory reports: I
250
II
350
III
450
IV
550
Laboratory notebook
~ 900
Pre-lab problems
~ 400 (LON-CAPA)
Final Exam
400
Total
~3300
Students earning 90% or more of the total points will receive a grade of 4.0. The dividing line
between 2.5 and 2.0 grades will be approximately 70% of the total points. The range between
90% and 70% will be divided into approximately equal parts for assigning grades of 3.5, 3.0, and
2.5. The dividing line between 1.0 and 0.0 grades will be about 55%. A passing grade will be
awarded to any student who completes and submits all Problem Sets, Lab Reports and
Notebooks on time, participates in all laboratory sessions (except for excused absences), and
earns at least 50% of the points.
Note: Reports (both a printed copy and the “text only” electronic submission) are due by 2:00 p.m. on the day listed in
the Schedule. Reports submitted after the due time/date will not receive any credit. Put all reports, unstapled,
in a large envelope with your name and section number on the outside and place the envelope in the wooden
“Assignment Box” in Room 113. Submit the “text only” copy of your report to the D2L dropbox for your section
by 2:00 p.m. on the day listed in the Schedule.
Notebooks are due at 9:00 a.m. on the day listed in the schedule and those submitted on time will be available for
pick-up after lecture the same day. Late notebooks will incur a 20 point per hour penalty and may not be
available for pick up until the following day. Notebooks submitted after 2:00 p.m. will receive no credit, but will be
corrected, and will be available for pick-up the following day.